R - How to avoid loop in list of files

Question

My current learning goal in R is to avoid for loops. I very often have to list the files in a directory (or loops through directories) to perform diverse operations on those files.

One example of my task is the following: I have to invoke a system application called cdo to merge two files. The syntax of this command is, let's say: cdo merge input_file1 input_file2 output_file.

My current R code looks like this:

# set lists of files
u.files <- c("uas_Amon_ACCESS1-3.nc", "uas_Amon_CMCC-CESM.nc", "uas_Amon_CMCC-CESM.nc")
v.files <- c("vas_Amon_ACCESS1-3.nc", "vas_Amon_CMCC-CESM.nc", "vas_Amon_CMCC-CESM.nc")

for (i in 1:length(u.files)) {

  # set input file 1 to use on cdo
  input1 <- paste(u.files[i], sep='')

  # set input file 2 to use on cdo
  input2 <- paste(v.files[i], sep='')

  # set output file to use on cdo
  output <- paste('output_', u.files[i], sep='') 

  # assemble the command string 
  comm <- paste('cdo merge', input1, input2, output, collapse='')

  # submit the command
  system(comm)

}

which works ok although does not look that good.

However, I often times hear people saying that for loops in R are slow and should be avoided as much as possible.

Is there any way to avoid the for loops and make the code more efficient/legible in cases like this?

Answer 1

This is more R-idiomatic:

u.files <- c("uas_Amon_ACCESS1-3.nc", "uas_Amon_CMCC-CESM.nc", "uas_Amon_CMCC-CESM.nc")
v.files <- c("vas_Amon_ACCESS1-3.nc", "vas_Amon_CMCC-CESM.nc", "vas_Amon_CMCC-CESM.nc")
output <- paste('output_', u.files, sep='')
comm <- paste('cdo merge', u.files, v.files, output)
lapply(comm,system)

Remember that most functions are vectorized in R, so you don't have to call paste for each iteration in the loop. At the end you obtain a vector of commands and execute one by one through lapply in the last line.